| dataset_type |
Allowable Value |
The specific type of dataset being produced. |
10X Multiome 2D Imaging Mass Cytometry ATACseq Auto-fluorescence Cell DIVE CODEX Confocal CosMx CyCIF DBiT DESI Enhanced Stimulated Raman Spectroscopy (SRS) GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology LC-MS Light Sheet MALDI MERFISH MIBI Molecular Cartography MUSIC nanoSPLITS PhenoCycler Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) SIMS SNARE-seq2 Stereo-seq Thick section Multiphoton MxIF Visium (no probes) Visium (with probes) Xenium |
True |
| analyte_class |
Allowable Value |
Analytes are the target molecules being measured with the assay. |
Chromatin DNA DNA + RNA Endogenous fluorophores Fluorochrome Lipid Metabolite Nucleic acid and protein Peptide Polysaccharide Protein RNA |
True |
| acquisition_instrument_vendor |
Allowable Value |
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. |
Akoya Biosciences Andor BGI Genomics Bruker Cytiva Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Motic NanoString Resolve Biosciences Sciex Standard BioTools (Fluidigm) Thermo Fisher Scientific Zeiss Microscopy |
True |
| acquisition_instrument_model |
Allowable Value |
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. |
Aperio AT2 Aperio CS2 Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 BZ-X710 BZ-X800 BZ-X810 CosMx Spatial Molecular Imager Custom: Multiphoton Digital Spatial Profiler DM6 B DNBSEQ-T7 EVOS M7000 HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 Lightsheet 7 MALDI timsTOF Flex Prototype MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 NovaSeq 6000 NovaSeq X NovaSeq X Plus Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 STELLARIS 5 TissueScope LE Slide Scanner Unknown VS200 Slide Scanner Xenium Analyzer Zyla 4.2 sCMOS |
True |
| source_storage_duration_value |
Numeric |
How long was the source material stored, prior to this sample being processed? For assays applied to tissue sections, this would be how long the tissue section (e.g., slide) was stored, prior to the assay beginning (e.g., imaging). For assays applied to suspensions such as sequencing, this would be how long the suspension was stored before library construction began. |
|
True |
| source_storage_duration_unit |
Allowable Value |
The time duration unit of measurement |
hour month day minute year |
True |
| time_since_acquisition_instrument_calibration_value |
Numeric |
The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture. |
|
False |
| time_since_acquisition_instrument_calibration_unit |
Allowable Value |
The time unit of measurement |
Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows |
False |
| preparation_protocol_doi |
Textfield |
DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 |
|
True |
| is_targeted |
Allowable Value |
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay (“Yes” or “No”). The CODEX analyte is protein. |
Yes No |
True |
| contributors_path |
Textfield |
The path to the file with the ORCID IDs for all contributors of this dataset (e.g., “./extras/contributors.tsv” or “./contributors.tsv”). This is an internal metadata field that is just used for ingest. |
|
True |
| data_path |
Textfield |
The top level directory containing the raw and/or processed data. For a single dataset upload this might be “.” where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called “TEST001-RK” use syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2” in which “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field that is just used for ingest. |
|
True |
| parent_sample_id |
Textfield |
Unique SenNet or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102 |
|
True |
| mapped_area_value |
Numeric |
For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured. |
|
False |
| mapped_area_unit |
Allowable Value |
The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2. |
um^2 mm^2 |
False |
| permeabilization_time_value |
Numeric |
Permeabilization time used for this tissue section. |
|
False |
| permeabilization_time_unit |
Allowable Value |
The unit for the permeabilization time. |
minute |
False |
| slide_id |
Textfield |
A unique ID denoting the slide used. This allows users the ability to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers. |
|
True |
| target_retrieval_incubation_temperature |
Numeric |
Will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays. |
|
False |
| target_retrieval_incubation_time_value |
Numeric |
The duration for which a sample is exposed to a target retrieval solution. |
|
False |
| target_retrieval_incubation_time_unit |
Allowable Value |
The units for target retrieval incubation time value. |
minute |
False |
| proteinasek_concentration |
Numeric |
The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml). |
|
False |
| proteinasek_incubation_time_value |
Numeric |
The duration for which a sample is exposed to Proteinase K. |
|
False |
| proteinasek_incubation_time_unit |
Allowable Value |
The units for proteinaseK incubation time value. |
minute |
False |
| probe_hybridization_time_value |
Numeric |
How long was the oligo-conjugated RNA or oligo-conjugated antibody probes hybridized with the sample? |
|
False |
| probe_hybridization_time_unit |
Allowable Value |
The units for probe hybridization time value. |
Hour Minute |
False |
| oligo_probe_panel |
Allowable Value |
This is the probe panel used to target genes and/or proteins. In cases where there is a core panel and add-on modules, the core panel should be selected here. If additional panels are used, then they must be included in the “additional_panels_used.csv” file that’s uploaded with the dataset. |
10x Genomics; Chromium Fixed RNA Kit Human Transcriptome 4 rxns x 1 BC; PN 1000474 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit 16 rxns; PN 1000420 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit 64 rxns; PN 1000456 10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466 10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363 10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365 Custom NanoString Technologies; GeoMx Human Whole Transcriptome Atlas 4 slides; PN GMX-RNA-NGS-HuWTA-4 NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas 4 slides; PN GMX-RNA-NGS-MsWTA-4 |
True |
| is_custom_probes_used |
Allowable Value |
State (“Yes” or “No”) whether custom RNA or antibody probes were used. If custom probes were used, they must be listed in the “custom_probe_set.csv” file. |
Yes No |
True |
| number_of_panel_targets |
Numeric |
How many genes, RNA isoforms or RNA regions are targeted by probes. |
|
True |
| roi_label |
Textfield |
A label for the region of interest (ROI). For Xenium, Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the “Initial Dataset” spreadsheet (download from within Data Analysis Suite). |
|
False |
| anatomical_structure_label |
Textfield |
The overarching anatomical structure. |
|
False |
| anatomical_structure_id |
Textfield |
The ontology ID for the parent structure. Typically this would be an UBERON ID. |
|
False |
| non_global_files |
Textfield |
A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the “TOP/non-global/” directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be “./lab_processed/images/1-tissue-boundary.geojson”. After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree. This field is used for internal SenNet processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee |
|
False |
| number_of_additional_stains |
Numeric |
This would be minimally 2 (always include DAPI and polyT) and can include 6 more. |
|
True |
| metadata_schema_id |
Textfield |
The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |
|
True |
